Results (PhD Chapter 2)
Section 2/2
This series of files compile all analyses done during Chapter 2:
- Section 1 presents indices of influence calculations.
- Section 2 presents HMSC and regressions results.
All analyses have been done with R 3.6.3.
Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it
To assess Section 1, click here.
To go back to the summary page, click here.
Sources of activity considered for the analyses:
- aquaculture influence: AquaInf
- city influence: CityInf
- industries influence: InduInf
- dredging collecting zones: CollDred
- dredging dumping zones: DumpDred
- commercial ships mooring site: MoorShip
- commercial ships traffic routes: TrafShip
- rainwater sewers: RainSew
- wastewater sewers: WastSew
- city wharves: CityWha
- industries wharves: InduWha
Fisheries data considered for the analyses (expressed as number of fishing events or kilograms of collected individuals for each gear):
| Gear | Code | Years | Events | Species |
|---|---|---|---|---|
| Trap | TrapFish | 2010-2015 | 1061 | Buccinum sp., Cancer irroratus, Chionoecetes opilio, Homarus americanus |
| Bottom-trawl | TrawFish | 2013-2014 | 2 | Pandalus borealis |
| Net | NetFish | 2010 | 5 | Clupea harengus, Gadus morhua |
| Dredge | DredFish | 2010-2014 | 21 | Mactromeris polynyma |
1. Explorations
1.1. Relationships between parameters
This section explores relationships between each pair of parameters or AH distances.
Fist, we can compute the Spearman’s correlation between each parameter.
| Â | om | gravel | sand | silt | clay | arsenic | cadmium | chromium | copper | iron | manganese | mercury | lead | zinc | S | N | H | J | aquaculture | city | dredging_collect | dredging_dump | industry | shipping_mooring | shipping_traffic | sewers_rain | sewers_waste | wharves_city | wharves_industry | fisheries_trap | fisheries_trawl | fisheries_net | fisheries_dredge | cumulative_influence |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| om | 1 | -0.379 | -0.708 | 0.68 | 0.023 | 0.57 | 0.486 | 0.606 | 0.593 | 0.586 | 0.568 | 0.537 | 0.587 | 0.605 | -0.026 | -0.121 | 0.122 | 0.136 | -0.41 | -0.032 | 0.43 | 0.308 | 0.219 | 0.518 | 0.291 | 0.24 | 0.401 | -0.073 | 0.365 | -0.501 | -0.227 | -0.025 | -0.282 | 0.253 |
| gravel | -0.379 | 1 | 0.186 | -0.471 | 0.099 | -0.127 | -0.23 | -0.194 | -0.23 | -0.232 | -0.199 | -0.207 | -0.169 | -0.235 | 0.029 | 0.007 | 0.012 | 0.07 | 0.143 | -0.069 | -0.16 | -0.08 | -0.175 | -0.217 | -0.02 | 0.001 | -0.073 | -0.06 | -0.166 | 0.171 | 0.229 | -0.025 | 0.09 | -0.124 |
| sand | -0.708 | 0.186 | 1 | -0.788 | -0.308 | -0.648 | -0.504 | -0.587 | -0.483 | -0.407 | -0.524 | -0.611 | -0.588 | -0.529 | 0.059 | 0.084 | 0.031 | -0.027 | 0.432 | 0.278 | -0.17 | -0.102 | -0.002 | -0.42 | -0.169 | -0.31 | -0.469 | 0.324 | -0.17 | 0.48 | 0.099 | -0.017 | 0.243 | -0.054 |
| silt | 0.68 | -0.471 | -0.788 | 1 | 0.05 | 0.548 | 0.482 | 0.506 | 0.441 | 0.362 | 0.449 | 0.566 | 0.519 | 0.493 | -0.054 | -0.013 | -0.068 | -0.055 | -0.409 | -0.151 | 0.178 | 0.079 | 0.045 | 0.423 | 0.083 | 0.247 | 0.391 | -0.196 | 0.175 | -0.463 | -0.187 | -0.058 | -0.259 | 0.071 |
| clay | 0.023 | 0.099 | -0.308 | 0.05 | 1 | 0.208 | 0.095 | 0.129 | 0.11 | 0.062 | 0.144 | 0.052 | 0.15 | 0.107 | -0.098 | -0.076 | -0.044 | 0.02 | -0.059 | -0.02 | 0.016 | 0.02 | 0.025 | 0.004 | 0.012 | 0.241 | 0.238 | -0.032 | 0.037 | -0.092 | -0.071 | -0.044 | -0.066 | 0.066 |
| arsenic | 0.57 | -0.127 | -0.648 | 0.548 | 0.208 | 1 | 0.797 | 0.862 | 0.791 | 0.656 | 0.78 | 0.707 | 0.902 | 0.87 | -0.266 | -0.149 | -0.193 | 0.008 | -0.657 | -0.067 | 0.216 | 0.076 | 0.059 | 0.659 | 0.213 | 0.522 | 0.71 | -0.158 | 0.213 | -0.585 | -0.295 | 0.093 | -0.463 | 0.169 |
| cadmium | 0.486 | -0.23 | -0.504 | 0.482 | 0.095 | 0.797 | 1 | 0.818 | 0.694 | 0.564 | 0.717 | 0.75 | 0.886 | 0.853 | -0.308 | -0.042 | -0.291 | -0.133 | -0.784 | -0.015 | 0.185 | -0.085 | -0.002 | 0.728 | 0.038 | 0.467 | 0.701 | -0.14 | 0.141 | -0.45 | -0.38 | -0.055 | -0.508 | 0.089 |
| chromium | 0.606 | -0.194 | -0.587 | 0.506 | 0.129 | 0.862 | 0.818 | 1 | 0.909 | 0.818 | 0.917 | 0.753 | 0.92 | 0.939 | -0.331 | -0.167 | -0.273 | -0.041 | -0.729 | -0.02 | 0.436 | 0.102 | 0.262 | 0.733 | 0.343 | 0.596 | 0.764 | -0.103 | 0.409 | -0.396 | -0.417 | 0.155 | -0.575 | 0.346 |
| copper | 0.593 | -0.23 | -0.483 | 0.441 | 0.11 | 0.791 | 0.694 | 0.909 | 1 | 0.808 | 0.842 | 0.715 | 0.872 | 0.952 | -0.298 | -0.172 | -0.225 | -0.025 | -0.655 | 0.238 | 0.57 | 0.218 | 0.438 | 0.751 | 0.432 | 0.641 | 0.755 | 0.169 | 0.536 | -0.369 | -0.511 | 0.173 | -0.631 | 0.537 |
| iron | 0.586 | -0.232 | -0.407 | 0.362 | 0.062 | 0.656 | 0.564 | 0.818 | 0.808 | 1 | 0.878 | 0.461 | 0.664 | 0.785 | -0.377 | -0.273 | -0.251 | 0.034 | -0.616 | 0.114 | 0.651 | 0.324 | 0.508 | 0.67 | 0.623 | 0.579 | 0.675 | 0.061 | 0.644 | -0.342 | -0.415 | 0.15 | -0.655 | 0.583 |
| manganese | 0.568 | -0.199 | -0.524 | 0.449 | 0.144 | 0.78 | 0.717 | 0.917 | 0.842 | 0.878 | 1 | 0.658 | 0.798 | 0.846 | -0.287 | -0.096 | -0.261 | -0.085 | -0.758 | -0.02 | 0.557 | 0.208 | 0.422 | 0.769 | 0.497 | 0.671 | 0.823 | -0.082 | 0.562 | -0.356 | -0.516 | 0.182 | -0.662 | 0.484 |
| mercury | 0.537 | -0.207 | -0.611 | 0.566 | 0.052 | 0.707 | 0.75 | 0.753 | 0.715 | 0.461 | 0.658 | 1 | 0.845 | 0.755 | -0.234 | -0.084 | -0.199 | -0.075 | -0.725 | -0.064 | 0.237 | -0.044 | 0.052 | 0.731 | 0.132 | 0.509 | 0.703 | -0.142 | 0.195 | -0.454 | -0.393 | 0.034 | -0.464 | 0.143 |
| lead | 0.587 | -0.169 | -0.588 | 0.519 | 0.15 | 0.902 | 0.886 | 0.92 | 0.872 | 0.664 | 0.798 | 0.845 | 1 | 0.939 | -0.304 | -0.135 | -0.252 | -0.051 | -0.707 | 0.029 | 0.316 | 0.049 | 0.129 | 0.738 | 0.21 | 0.599 | 0.769 | -0.065 | 0.277 | -0.488 | -0.383 | 0.071 | -0.51 | 0.252 |
| zinc | 0.605 | -0.235 | -0.529 | 0.493 | 0.107 | 0.87 | 0.853 | 0.939 | 0.952 | 0.785 | 0.846 | 0.755 | 0.939 | 1 | -0.32 | -0.145 | -0.253 | -0.056 | -0.718 | 0.151 | 0.471 | 0.151 | 0.306 | 0.79 | 0.341 | 0.603 | 0.764 | 0.067 | 0.429 | -0.454 | -0.464 | 0.112 | -0.611 | 0.413 |
| S | -0.026 | 0.029 | 0.059 | -0.054 | -0.098 | -0.266 | -0.308 | -0.331 | -0.298 | -0.377 | -0.287 | -0.234 | -0.304 | -0.32 | 1 | 0.561 | 0.705 | -0.052 | 0.347 | -0.142 | -0.158 | 0.077 | -0.114 | -0.253 | -0.045 | -0.313 | -0.331 | -0.069 | -0.151 | 0.158 | 0.278 | 0.088 | 0.377 | -0.145 |
| N | -0.121 | 0.007 | 0.084 | -0.013 | -0.076 | -0.149 | -0.042 | -0.167 | -0.172 | -0.273 | -0.096 | -0.084 | -0.135 | -0.145 | 0.561 | 1 | -0.041 | -0.683 | -0.006 | -0.061 | -0.162 | -0.17 | -0.139 | -0.021 | -0.111 | -0.115 | -0.067 | -0.061 | -0.169 | 0.181 | -0.017 | -0.001 | 0.066 | -0.12 |
| H | 0.122 | 0.012 | 0.031 | -0.068 | -0.044 | -0.193 | -0.291 | -0.273 | -0.225 | -0.251 | -0.261 | -0.199 | -0.252 | -0.253 | 0.705 | -0.041 | 1 | 0.598 | 0.373 | -0.087 | -0.015 | 0.285 | 0.026 | -0.243 | -0.028 | -0.305 | -0.329 | -0.003 | -0.015 | 0.031 | 0.254 | -0.027 | 0.399 | -0.084 |
| J | 0.136 | 0.07 | -0.027 | -0.055 | 0.02 | 0.008 | -0.133 | -0.041 | -0.025 | 0.034 | -0.085 | -0.075 | -0.051 | -0.056 | -0.052 | -0.683 | 0.598 | 1 | 0.186 | 0.01 | 0.053 | 0.236 | 0.073 | -0.129 | -0.021 | -0.106 | -0.147 | 0.035 | 0.061 | -0.136 | 0.087 | -0.05 | 0.182 | -0.017 |
| aquaculture | -0.41 | 0.143 | 0.432 | -0.409 | -0.059 | -0.657 | -0.784 | -0.729 | -0.655 | -0.616 | -0.758 | -0.725 | -0.707 | -0.718 | 0.347 | -0.006 | 0.373 | 0.186 | 1 | -0.069 | -0.306 | 0.13 | -0.168 | -0.828 | -0.183 | -0.596 | -0.84 | 0.079 | -0.27 | 0.383 | 0.66 | 0.098 | 0.754 | -0.206 |
| city | -0.032 | -0.069 | 0.278 | -0.151 | -0.02 | -0.067 | -0.015 | -0.02 | 0.238 | 0.114 | -0.02 | -0.064 | 0.029 | 0.151 | -0.142 | -0.061 | -0.087 | 0.01 | -0.069 | 1 | 0.368 | 0.051 | 0.292 | 0.298 | 0.133 | 0.324 | 0.161 | 0.969 | 0.255 | -0.069 | -0.397 | 0.194 | -0.487 | 0.564 |
| dredging_collect | 0.43 | -0.16 | -0.17 | 0.178 | 0.016 | 0.216 | 0.185 | 0.436 | 0.57 | 0.651 | 0.557 | 0.237 | 0.316 | 0.471 | -0.158 | -0.162 | -0.015 | 0.053 | -0.306 | 0.368 | 1 | 0.722 | 0.895 | 0.587 | 0.804 | 0.545 | 0.52 | 0.435 | 0.956 | -0.126 | -0.468 | 0.069 | -0.588 | 0.895 |
| dredging_dump | 0.308 | -0.08 | -0.102 | 0.079 | 0.02 | 0.076 | -0.085 | 0.102 | 0.218 | 0.324 | 0.208 | -0.044 | 0.049 | 0.151 | 0.077 | -0.17 | 0.285 | 0.236 | 0.13 | 0.051 | 0.722 | 1 | 0.732 | 0.181 | 0.655 | 0.169 | 0.144 | 0.17 | 0.764 | -0.135 | -0.045 | -0.129 | -0.101 | 0.581 |
| industry | 0.219 | -0.175 | -0.002 | 0.045 | 0.025 | 0.059 | -0.002 | 0.262 | 0.438 | 0.508 | 0.422 | 0.052 | 0.129 | 0.306 | -0.114 | -0.139 | 0.026 | 0.073 | -0.168 | 0.292 | 0.895 | 0.732 | 1 | 0.358 | 0.741 | 0.485 | 0.416 | 0.371 | 0.946 | 0.062 | -0.508 | 0.027 | -0.424 | 0.833 |
| shipping_mooring | 0.518 | -0.217 | -0.42 | 0.423 | 0.004 | 0.659 | 0.728 | 0.733 | 0.751 | 0.67 | 0.769 | 0.731 | 0.738 | 0.79 | -0.253 | -0.021 | -0.243 | -0.129 | -0.828 | 0.298 | 0.587 | 0.181 | 0.358 | 1 | 0.409 | 0.591 | 0.766 | 0.239 | 0.499 | -0.518 | -0.644 | 0.091 | -0.787 | 0.511 |
| shipping_traffic | 0.291 | -0.02 | -0.169 | 0.083 | 0.012 | 0.213 | 0.038 | 0.343 | 0.432 | 0.623 | 0.497 | 0.132 | 0.21 | 0.341 | -0.045 | -0.111 | -0.028 | -0.021 | -0.183 | 0.133 | 0.804 | 0.655 | 0.741 | 0.409 | 1 | 0.569 | 0.45 | 0.232 | 0.834 | -0.052 | -0.204 | 0.336 | -0.501 | 0.828 |
| sewers_rain | 0.24 | 0.001 | -0.31 | 0.247 | 0.241 | 0.522 | 0.467 | 0.596 | 0.641 | 0.579 | 0.671 | 0.509 | 0.599 | 0.603 | -0.313 | -0.115 | -0.305 | -0.106 | -0.596 | 0.324 | 0.545 | 0.169 | 0.485 | 0.591 | 0.569 | 1 | 0.891 | 0.279 | 0.572 | -0.18 | -0.55 | 0.296 | -0.764 | 0.667 |
| sewers_waste | 0.401 | -0.073 | -0.469 | 0.391 | 0.238 | 0.71 | 0.701 | 0.764 | 0.755 | 0.675 | 0.823 | 0.703 | 0.769 | 0.764 | -0.331 | -0.067 | -0.329 | -0.147 | -0.84 | 0.161 | 0.52 | 0.144 | 0.416 | 0.766 | 0.45 | 0.891 | 1 | 0.068 | 0.523 | -0.36 | -0.629 | 0.047 | -0.781 | 0.502 |
| wharves_city | -0.073 | -0.06 | 0.324 | -0.196 | -0.032 | -0.158 | -0.14 | -0.103 | 0.169 | 0.061 | -0.082 | -0.142 | -0.065 | 0.067 | -0.069 | -0.061 | -0.003 | 0.035 | 0.079 | 0.969 | 0.435 | 0.17 | 0.371 | 0.239 | 0.232 | 0.279 | 0.068 | 1 | 0.331 | -0.006 | -0.324 | 0.263 | -0.411 | 0.637 |
| wharves_industry | 0.365 | -0.166 | -0.17 | 0.175 | 0.037 | 0.213 | 0.141 | 0.409 | 0.536 | 0.644 | 0.562 | 0.195 | 0.277 | 0.429 | -0.151 | -0.169 | -0.015 | 0.061 | -0.27 | 0.255 | 0.956 | 0.764 | 0.946 | 0.499 | 0.834 | 0.572 | 0.523 | 0.331 | 1 | -0.066 | -0.45 | 0.074 | -0.551 | 0.881 |
| fisheries_trap | -0.501 | 0.171 | 0.48 | -0.463 | -0.092 | -0.585 | -0.45 | -0.396 | -0.369 | -0.342 | -0.356 | -0.454 | -0.488 | -0.454 | 0.158 | 0.181 | 0.031 | -0.136 | 0.383 | -0.069 | -0.126 | -0.135 | 0.062 | -0.518 | -0.052 | -0.18 | -0.36 | -0.006 | -0.066 | 1 | 0.256 | 0.038 | 0.267 | -0.035 |
| fisheries_trawl | -0.227 | 0.229 | 0.099 | -0.187 | -0.071 | -0.295 | -0.38 | -0.417 | -0.511 | -0.415 | -0.516 | -0.393 | -0.383 | -0.464 | 0.278 | -0.017 | 0.254 | 0.087 | 0.66 | -0.397 | -0.468 | -0.045 | -0.508 | -0.644 | -0.204 | -0.55 | -0.629 | -0.324 | -0.45 | 0.256 | 1 | 0.032 | 0.605 | -0.454 |
| fisheries_net | -0.025 | -0.025 | -0.017 | -0.058 | -0.044 | 0.093 | -0.055 | 0.155 | 0.173 | 0.15 | 0.182 | 0.034 | 0.071 | 0.112 | 0.088 | -0.001 | -0.027 | -0.05 | 0.098 | 0.194 | 0.069 | -0.129 | 0.027 | 0.091 | 0.336 | 0.296 | 0.047 | 0.263 | 0.074 | 0.038 | 0.032 | 1 | -0.173 | 0.337 |
| fisheries_dredge | -0.282 | 0.09 | 0.243 | -0.259 | -0.066 | -0.463 | -0.508 | -0.575 | -0.631 | -0.655 | -0.662 | -0.464 | -0.51 | -0.611 | 0.377 | 0.066 | 0.399 | 0.182 | 0.754 | -0.487 | -0.588 | -0.101 | -0.424 | -0.787 | -0.501 | -0.764 | -0.781 | -0.411 | -0.551 | 0.267 | 0.605 | -0.173 | 1 | -0.647 |
| cumulative_influence | 0.253 | -0.124 | -0.054 | 0.071 | 0.066 | 0.169 | 0.089 | 0.346 | 0.537 | 0.583 | 0.484 | 0.143 | 0.252 | 0.413 | -0.145 | -0.12 | -0.084 | -0.017 | -0.206 | 0.564 | 0.895 | 0.581 | 0.833 | 0.511 | 0.828 | 0.667 | 0.502 | 0.637 | 0.881 | -0.035 | -0.454 | 0.337 | -0.647 | 1 |
For the regressions, several types of models were considered: linear, quadratic, exponential and logarithmic. Only linear and quadratic models were implemented as there are some bugs with the calculation of the others. The model with the highest \(R^{2}\) is presented on each plot.
AquaInf
CityInf
InduInf
CollDred
DumpDred
MoorShip
TrafShip
RainSew
WastSew
CityWha
InduWha
TrapFish
TrawFish
NetFish
DredFish
Cumulative Influence
1.2. Species abundances by cumulative influence group
| Phylum | low | bad | moderate | high | good |
|---|---|---|---|---|---|
| Annelida | NA | 29.5 | 31.6 | 25.3 | NA |
| Arthropoda | NA | 20.3 | 48.3 | 40.8 | NA |
| Cnidaria | NA | 0.1 | 0 | 0 | NA |
| Echinodermata | NA | 13.5 | 1.32 | 4.09 | NA |
| Mollusca | NA | 10.8 | 13.3 | 16.2 | NA |
| Nematoda | NA | 22.7 | 10.4 | 1.32 | NA |
| Nemertea | NA | 0 | 0.211 | 0 | NA |
| Sipuncula | NA | 0 | 0.224 | 0.545 | NA |
2. Hierarchical Modelling of Species Communities
We will use the probabilities and indices of influences calculated in Section 1 here. The aim is to obtain predictive models for the benthic communities, based on the abiotic parameters and the human activities.
HMSC models have been developped in a dedicated script, and the R workspace has been imported here.
First, we initiate the HMSC model with the chosen data, priors and parameters.
Here are the diagnostics to evaluate each model’s quality.
Human activities
Trace plots
Explanatory power
Confidence intervals
Variance partitioning
Habitat parameters
Trace plots
Explanatory power
Confidence intervals
Variance partitioning
All variables
Trace plots
Explanatory power
Confidence intervals
Variance partitioning
Finally, we can predict the values of our parameters within BSI.